Sam:LabNotes/Microbiome-new/2011-4-25
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Taxonomic analysis on proportioned raw reads and failed-to-align(bowtie) reads on E.coli SAG Illumina and Nextera libraries
Background
- Since the blastn + MEGAN works very well on failed-to-align reads taxonomic analysis (Test did on E.coli SAG Nextera library). I am planing to extend the same method to characterize the raw reads.
- Compare the the results with the result from bowtie mapping, then quantify how many false negative E.coli reads are mis-called by bowtie mapping.
- Also, I will compare the different sampling size (10,000 reads vs. 1000 reads) and see if there is bias existed due to my sampling threshold.
Objectives
- Analyze the taxonomic distribution on raw reads for E.coli SAGs Ill and NX library data. Compare the conclusion with bowtie's conclusion.
- Test if 10000-read sample's conclusion is different from 1000-read sampling.
- Test if Nextra library generate more no-hit or contamination then standard Illumina library.
- Compare the taxonomic distribution on (1)raw reads (2) failed-to-align reads
- NOTE: Since I didn't use the same source of the amplified MDA sample to generate Ill and NX library for a side-by-side comparison, it is not convincing to judge which library construction protocol is "cleaner". However if the different is on the abundance of the "no hit", then it is not due to the contamination issue.
Procedures
- Sample 1M reads from raw reads and failed-to-align reads for both Ecoli SAG Illumina (101123_HL083_s4_Ecoli_IllLib) and Nextera(110120_HL087_s4_Ecoli_NexLib) sequencing data.
- Using the new perl script: fastq-data-sampler-v2-hc
samchiang@genemapster:~/Scripts$ perl fastq-data-sampler-v2-hc /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID2.txt /media/disk-1/samchiang/Raw-Read-Complete/101123_HL083/HC-MDA-Ecoli-SAGs-Ind1to8-PE/s_4_1and2_ID2.1Mreads 1000000 &